Metal-dielectric nanostructures consisting of Ag nanoparticles synthesized within a mesoporous silicon matrix are exploited for single molecule detection by surface-enhanced resonance Raman scattering (SERRS). The morphology is controlled yielding plasmonic resonances in the visible-near-infrared range. Enhanced Raman activity of the substrates are tested using Cy3 and R6G dyes as probe molecules. Tuning the particle plasmonic resonance close to the molecule electronic resonance, we demonstrate Raman enhancements larger than 1010. Time resolved Raman spectroscopy at very low molecule concentration yields intensity fluctuations which can be mainly ascribed to a charge transfer-enhancement mediated by the molecules diffusion between different sites on Ag particles.